signeR

DOI: 10.18129/B9.bioc.signeR  

Empirical Bayesian approach to mutational signature discovery

Bioconductor version: Release (3.17)

The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variaton (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.

Author: Rafael Rosales, Rodrigo Drummond, Renan Valieris, Israel Tojal da Silva

Maintainer: Renan Valieris <renan.valieris at accamargo.org.br>

Citation (from within R, enter citation("signeR")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("signeR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("signeR")

 

HTML R Script signeR
HTML R Script signeRFlow
PDF   Reference Manual
Text   NEWS

Details

biocViews GenomicVariation, Software, SomaticMutation, StatisticalMethod, Visualization
Version 2.2.1
In Bioconductor since BioC 3.4 (R-3.3) (7 years)
License GPL-3
Depends R (>= 3.0.2), VariantAnnotation, NMF
Imports BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat, survivalAnalysis, future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada, future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv, reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble, readr, shiny, shinydashboard, shinycssloaders, shinyWidgets, bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer, BSgenome
LinkingTo Rcpp, RcppArmadillo (>= 0.7.100)
Suggests knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown
SystemRequirements C++11
Enhances
URL https://github.com/rvalieris/signeR
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package signeR_2.2.1.tar.gz
Windows Binary signeR_2.2.1.zip
macOS Binary (x86_64) signeR_2.2.1.tgz
macOS Binary (arm64) signeR_2.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/signeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/signeR
Bioc Package Browser https://code.bioconductor.org/browse/signeR/
Package Short Url https://bioconductor.org/packages/signeR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive

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